Origin IGS: tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggtggagtctcctttatttttgaaatgaagagttggaaattttagtaaaaaatcctgctcttaaattttcttaatcgcttacattgtagcatattttcattaattttgaaagaggttacctagaaaacgatgaaatacttttcaaggcattgtttcaaggatttcaagatggtaaagttgaaatgcgggattaaaaaaagaccaaagcaaggcttggtctggaaagctaatttatca Mask Tandem Repeat Region ================================================ tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Find is-nt database================================================ Query_seq: SSA_1203:SSA_1204|SSA_1203:SSA_1204:hypothetical protein:Phosphoglucomutase:->->:1227689..1227926 238 tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1203:SSA_1204|SSA_1203:SSA_1204:hypothetical protein:Phosphoglucomutase:->->:1227689..1227926 238 tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1203:SSA_1204|SSA_1203:SSA_1204:hypothetical protein:Phosphoglucomutase:->->:1227689..1227926 238 tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 47 End: 145 .............................................. D R M E V K G D Q F G Q F L A K F L I E D N E L Y G R E F N I F M ............................................................................................. Protein_Len: 36 Strand: - Start: 1 End: 108 S L N A K W V L G Q K P R K K I G C K L K V M K F D K F C H R S F Y K M .................................................................................................................................. tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 126 End: 155 .............................................................................................................................CTTTCAAAATTAATGAAAATATGCTACAAT................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1203:SSA_1204|SSA_1203:SSA_1204:hypothetical protein:Phosphoglucomutase:->->:1227689..1227926 238 tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Intra-Species Hit: Count: 1 Min: 1 Max: 238 Len: 238 Subject: NC_009009_SSA_1203_SSA_1204|hypothetical protein:Phosphoglucomutase|POSITIVE:POSITIVE|[1227689, 1227926]|238 HSP 1 e-value: 1.0E-120 bit: 430.0 Len: 238 Query Start:1 Query End:238 Subject Strand: POSITIVE Subject Start: 1 Subject End: 238 tgataaattagctttccagaccaagccttgctttggtcnnnnnnnaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct tgataaattagctttccagaccaagccttgctttggtctttttttaatcccgcatttcaactttaccatcttgaaatccttgaaacaatgccttgaaaagtatttcatcgttttctaggtaacctctttcaaaattaatgaaaatatgctacaatgtaagcgattaagaaaatttaagagcaggattttttactaaaatttccaactcttcatttcaaaaataaaggagactccacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAAUUAGCUUUCCAGACCAAGCCUUGCUUUGGUCUUUUUUUAAUCCCGCAUUUCAACUUUACCAUCUUGAAAUCCUUGAAACAAUGCCUUGAAAAGUAUUUCAUCGUUUUCUAGGUAACCUCUUUCAAAAUUAAUGAAAAUAUGCUACAAUGUAAGCGAUUAAGAAAAUUUAAGAGCAGGAUUUUUUACUAAAAUUUCCAACUCUUCAUUUCAAAAAUAAAGGAGACUCCACCU .........((.(((((.((((((((...)).)))))).((((((((((..((.(((((..((((......))))....((((((...(((((.((((((........).))))).))))).....))))))......)))))...(((......))).))))))))))))....(((((..(((..(((.....)))..)))..)))))...............)))))))...... (-40.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGGAGUCUCCUUUAUUUUUGAAAUGAAGAGUUGGAAAUUUUAGUAAAAAAUCCUGCUCUUAAAUUUUCUUAAUCGCUUACAUUGUAGCAUAUUUUCAUUAAUUUUGAAAGAGGUUACCUAGAAAACGAUGAAAUACUUUUCAAGGCAUUGUUUCAAGGAUUUCAAGAUGGUAAAGUUGAAAUGCGGGAUUAAAAAAAGACCAAAGCAAGGCUUGGUCUGGAAAGCUAAUUUAUCA ((((((..(((.....(((..(((((..((((((.(((..((((.....))))))).))))))..............(((........)))....)))))..)))......)))..)))))).......((((((.((((((((...........((..(.(((((((..........))))))).)..))........(((((((.((...))))))))))))))).)).)))))). (-49.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 58 15 183 122 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 312 70 21 76 7 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 289 54 11 205 146 NC_009009:SSA_0676|5end_Farnesyl_diphosphate_synthase,_putative_658598..658828_POSITIVE 286 130 82 189 130 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 284 54 13 161 114 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 282 55 11 185 132 NC_009009:SSA_1498|5end_50S_ribosomal_protein_L20,_putative_1504112..1504342_NEGATIVE 281 59 11 108 33 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 281 50 8 51 12 NC_009009:SSA_0046|5end_Adenylosuccinate_lyase,_putative_50894..51124_POSITIVE 276 36 7 54 30 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 276 60 11 220 163 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 273 60 11 108 50 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 270 50 8 66 31 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 267 70 23 92 34 NC_009009:SSA_0228|5end_hypothetical_protein_223363..223593_POSITIVE 259 41 9 175 139 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 257 59 18 206 158 NC_009009:SSA_0201|5end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_199825..200055_POSITIVE 256 55 11 54 9 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 255 67 21 70 19 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 254 207 177 35 10 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 254 69 21 91 32 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 253 58 11 102 52 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 50 7 139 90 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 282 55 11 140 87 NC_009009:SSA_1499|3end_50S_ribosomal_protein_L35,_putative_1504157..1504307_NEGATIVE 281 59 13 66 8 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 276 36 7 61 37 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 273 60 11 108 50 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 268 43 4 144 96 NC_009009:SSA_1687|3end_NADH-binding_ferric-oxidoreductase,_putative_1681823..1681973_POSITIVE 257 59 18 111 63 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 256 55 11 54 9 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 255 54 11 55 11 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 255 55 11 46 5 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 255 70 21 106 49 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 254 207 177 42 17 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 254 38 7 148 116 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 252 70 22 128 80 NC_009009:SSA_2194|3end_Nicotinamide_mononucleotide_transporter,_putative_2194848..2194998_NEGATIVE 251 40 16 48 21 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 248 59 11 133 88 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 245 60 18 147 97 NC_009009:SSA_0855|3end_O-acetylhomoserine_sulfhydrylase,_putative_843192..843342_POSITIVE 243 78 31 55 6 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 242 42 11 79 41 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 241 59 11 121 64 NC_009009:SSA_0739|3end_Carbamate_kinase,_putative_722114..722264_POSITIVE